TB-Profiler result

Run: ERR2229560
Summary

Run ID: ERR2229560

Sample name:

Date: 31-03-2023 17:18:57

Number of reads: 1032443

Percentage reads mapped: 99.49

Strain: lineage4.8

Drug-resistance: Sensitive

Download CSV Download TXT Download PDF Download JSON
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 1.0
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction
gyrA 7362 p.Glu21Gln missense_variant 1.0
mshA 575265 c.-83C>T upstream_gene_variant 0.12
mshA 576108 p.Ala254Gly missense_variant 0.36
rpoB 760708 p.Asp301Val missense_variant 0.12
rpoC 766162 p.Asp931Glu missense_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776248 p.Ala745Ser missense_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304038 p.Pro370Ala missense_variant 0.12
fbiC 1304182 p.Ala418Thr missense_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
fabG1 1673349 c.-91G>C upstream_gene_variant 0.11
fabG1 1673359 c.-81T>C upstream_gene_variant 0.11
fabG1 1673361 c.-79C>G upstream_gene_variant 0.11
inhA 1674551 p.Ser117Tyr missense_variant 0.12
rpsA 1834735 c.1194C>T synonymous_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918725 c.786T>C synonymous_variant 0.11
katG 2155261 p.Val284Gly missense_variant 0.13
PPE35 2168322 p.Ile764Asn missense_variant 0.14
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169602 c.1011C>A synonymous_variant 0.14
PPE35 2170048 p.Leu189Val missense_variant 0.65
PPE35 2170053 p.Thr187Ser missense_variant 0.68
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2725936 c.-257G>A upstream_gene_variant 0.15
Rv2752c 3064831 p.Ala454Asp missense_variant 0.33
fbiD 3339734 p.Ala206Gly missense_variant 0.25
alr 3841546 c.-126C>A upstream_gene_variant 0.21
clpC1 4040094 p.Leu204Arg missense_variant 0.25
clpC1 4040129 c.576C>A synonymous_variant 0.12
clpC1 4040436 p.Leu90Pro missense_variant 0.11
embC 4240128 p.Gln89Arg missense_variant 0.11
embC 4241968 c.2106A>G synonymous_variant 0.14
embC 4241973 p.Val704Ala missense_variant 0.15
embC 4242283 p.Ser807Arg missense_variant 0.5
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4249618 c.3105C>G synonymous_variant 0.12
embB 4249661 p.Ala1050Ser missense_variant 0.17
aftB 4267943 p.Tyr298* stop_gained 0.25
aftB 4268943 c.-107C>A upstream_gene_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0